He made his professional debut for Landskrona in a match in Superettan 2001, same year as BoIS became runners-up and was promoted to Allsvenskan again.

To play some more matches, Malmqvist went on loan to the recently relegated Allsvenskan team Trelleborgs FF.

[5] Malmqvist returned to Landskrona in 2008, as a part of the campaign to reach Allsvenskan under the new coach Anders Linderoth.

[7] The following three years BoIS were coached by Henrik Larsson and Malmqvist continued in 2010 and 2011 in his role as a regular central defender and team captain.

Superettan 2013 became Linus Malmqvist last season as a player in Landskrona BoIS, after having had constant pain in the right ankle and lower leg for two years.